Acoustic telemetry residency analysis

Summary

Target folder: /Users/brittneyscannell/Desktop/actel

Timestamp: 2025-01-06 13:37:51.357207

Number of target tags: 53

Number of listed receivers: 27 (of which 13 had no detections)

Data time range: 2022-11-28 14:20:06 to 2024-10-02 14:33:45 (Asia/Riyadh).

Percentage of post-release valid detections: 100%

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Study area

Arrays with the same background belong to the same section. Release sites are marked with “R.S.”. Arrays connected with an arrow indicate that the animals can only pass in one direction.

Receiver stations

Station.name	Latitude	Longitude	Section	Array	Standard.name
AK1	25.67437	36.74693	Abu_Khalid	Abu_Khalid	St.1
AL2	25.53851	36.91802	Abu_Laheq	Abu_Laheq	St.2
AOG	25.65634	36.71978	Al_Osh_Al_Gharbi	Al_Osh_Al_Gharbi	St.3
AOS1	25.66300	36.76780	Al_Osh_Al_Sharqi	Al_Osh_Al_Sharqi	St.4
AOS2	25.66650	36.76420	Al_Osh_Al_Sharqi	Al_Osh_Al_Sharqi	St.5
AOS3	25.66431	36.75544	Al_Osh_Al_Sharqi	Al_Osh_Al_Sharqi	St.6
AOS4	25.66670	36.75832	Al_Osh_Al_Sharqi	Al_Osh_Al_Sharqi	St.7
AOS5	25.65846	36.75521	Al_Osh_Al_Sharqi	Al_Osh_Al_Sharqi	St.8
AOS6	25.66008	36.75787	Al_Osh_Al_Sharqi	Al_Osh_Al_Sharqi	St.9
AOS7	25.66210	36.76510	Al_Osh_Al_Sharqi	Al_Osh_Al_Sharqi	St.10
AOS8	25.66065	36.76154	Al_Osh_Al_Sharqi	Al_Osh_Al_Sharqi	St.11
Deep	25.56643	36.82818	QUMAN	QUMAN	St.12
GH01	25.56620	36.83358	QUMAN	QUMAN	St.13
GH02	25.56579	36.83349	QUMAN	QUMAN	St.14
GH03	25.56560	36.83309	QUMAN	QUMAN	St.15
GH04	25.56529	36.83291	QUMAN	QUMAN	St.16
GH05	25.56506	36.83265	QUMAN	QUMAN	St.17
GH07	25.56436	36.83241	QUMAN	QUMAN	St.18
GH08	25.56404	36.83226	QUMAN	QUMAN	St.19
GH09	25.56369	36.83213	QUMAN	QUMAN	St.20
GH10	25.56336	36.83201	QUMAN	QUMAN	St.21
GH11	25.56307	36.83185	QUMAN	QUMAN	St.22
GH12	25.56283	36.83162	QUMAN	QUMAN	St.23
GH13	25.56256	36.83142	QUMAN	QUMAN	St.24
Qu1	25.57283	36.84520	QUMAN	QUMAN	St.25
Qu10	25.53528	36.84713	QUMAN	QUMAN	St.26
Qu11	25.55508	36.86840	QUMAN	QUMAN	St.27
Qu12	25.55792	36.86718	QUMAN	QUMAN	St.28
Qu13	25.56872	36.83678	QUMAN	QUMAN	St.29
Qu14	25.54187	36.85135	QUMAN	QUMAN	St.30
Qu15	25.55065	36.86613	QUMAN	QUMAN	St.31
Qu2	25.56471	36.83258	QUMAN	QUMAN	St.32
Qu3	25.56224	36.83131	QUMAN	QUMAN	St.33
Qu4	25.53987	36.85668	QUMAN	QUMAN	St.34
Qu5	25.53457	36.83698	QUMAN	QUMAN	St.35
Qu6	25.54875	36.82483	QUMAN	QUMAN	St.36
Qu7	25.54185	36.82805	QUMAN	QUMAN	St.37
Qu8	25.56537	36.85785	QUMAN	QUMAN	St.38
Qu9	25.54550	36.86677	QUMAN	QUMAN	St.39
TB2	25.49917	36.99869	Turtle_Bay	Turtle_Bay	St.40

Deployments

Receiver	Array	Station.name	Standard.name	Start	Stop
488907.dpl.1	QUMAN	GH09	St.20	2022-11-28 09:53:00	2023-04-26 00:00:00
488907.dpl.2	QUMAN	Qu14	St.30	2023-04-26 13:18:00	2024-10-03 00:00:00
488908.dpl.1	QUMAN	GH12	St.23	2022-11-28 10:05:00	2023-04-26 00:00:00
488908.dpl.2	QUMAN	Qu1	St.25	2023-04-26 12:01:00	2024-09-30 00:00:00
488909.dpl.1	QUMAN	GH02	St.14	2022-11-28 08:50:00	2023-04-26 00:00:00
488909.dpl.2	QUMAN	Qu8	St.38	2023-04-26 14:26:00	2024-10-02 00:00:00
488910	QUMAN	Qu2	St.32	2022-11-28 11:33:00	2024-10-03 00:00:00
488911.dpl.1	QUMAN	GH03	St.15	2022-11-28 09:00:00	2023-04-26 00:00:00
488911.dpl.2	QUMAN	Qu11	St.27	2023-04-26 14:10:00	2024-10-03 00:00:00
488912.dpl.1	QUMAN	GH01	St.13	2022-11-28 08:45:00	2023-04-26 00:00:00
488912.dpl.2	QUMAN	Qu12	St.28	2023-04-26 14:17:00	2024-10-02 00:00:00
488913.dpl.1	QUMAN	GH08	St.19	2022-11-28 09:35:00	2023-04-26 00:00:00
488913.dpl.2	QUMAN	Qu10	St.26	2023-04-26 13:05:00	2024-09-27 00:00:00
488914.dpl.1	QUMAN	GH11	St.22	2022-11-28 10:00:00	2023-04-26 00:00:00
488914.dpl.2	QUMAN	Qu6	St.36	2023-04-26 12:27:00	2024-09-27 00:00:00
488915.dpl.1	QUMAN	GH07	St.18	2022-11-28 09:30:00	2023-04-26 00:00:00
488915.dpl.2	QUMAN	Qu4	St.34	2023-04-26 13:31:00	2024-09-30 00:00:00
488916.dpl.1	QUMAN	Deep	St.12	2022-11-28 10:35:00	2023-04-26 00:00:00
488916.dpl.2	QUMAN	Qu7	St.37	2023-04-26 12:40:00	2024-09-27 00:00:00
488917.dpl.1	QUMAN	GH10	St.21	2022-11-28 09:55:00	2023-04-26 00:00:00
488917.dpl.2	QUMAN	Qu5	St.35	2023-04-26 12:54:00	2024-09-27 00:00:00
488918.dpl.1	QUMAN	GH05	St.17	2022-11-28 09:17:00	2023-04-26 00:00:00
488918.dpl.2	QUMAN	Qu9	St.39	2023-04-26 13:39:00	2024-10-03 00:00:00
488919.dpl.1	QUMAN	GH04	St.16	2022-11-28 09:06:00	2023-04-26 00:00:00
488919.dpl.2	QUMAN	Qu15	St.31	2023-04-26 13:46:00	2024-10-03 00:00:00
488920.dpl.1	QUMAN	GH13	St.24	2022-11-28 10:10:00	2023-04-26 00:00:00
488920.dpl.2	QUMAN	Qu13	St.29	2023-04-26 11:47:00	2024-10-31 00:00:00
488921	QUMAN	Qu3	St.33	2022-11-28 11:20:00	2024-10-03 00:00:00
490788	Al_Osh_Al_Gharbi	AOG	St.3	2023-10-12 12:53:00	2024-10-28 04:30:00
490791	Al_Osh_Al_Sharqi	AOS6	St.9	2023-10-12 11:42:00	2024-10-26 11:19:00
490792	Al_Osh_Al_Sharqi	AOS2	St.5	2023-10-10 10:29:00	2024-08-07 16:37:00
490793	Al_Osh_Al_Sharqi	AOS1	St.4	2023-10-10 10:09:00	2024-10-26 00:00:00
490794	Al_Osh_Al_Sharqi	AOS4	St.7	2023-10-10 11:11:00	2024-10-28 06:22:00
490795	Al_Osh_Al_Sharqi	AOS3	St.6	2023-10-10 10:57:00	2024-10-27 05:52:00
490796	Al_Osh_Al_Sharqi	AOS5	St.8	2023-10-10 11:30:00	2024-10-28 06:08:00
490797	Turtle_Bay	TB2	St.40	2023-10-14 09:19:00	2024-02-18 11:54:00
490798	Abu_Khalid	AK1	St.1	2023-10-12 12:36:00	2024-10-28 05:07:00
490799	Abu_Laheq	AL2	St.2	2023-10-13 14:09:00	2024-10-28 08:09:00
490800	Al_Osh_Al_Sharqi	AOS7	St.10	2023-10-12 12:17:00	2024-10-26 10:17:00
490801	Al_Osh_Al_Sharqi	AOS8	St.11	2023-10-12 12:02:00	2024-10-26 10:58:00

Release sites

Station.name	Latitude	Longitude	Array	Type	Standard.name	n.Wild
E21	25.66883	36.75964	Al_Osh_Al_Sharqi	Release	E21	2
E20	25.65912	36.75592	Al_Osh_Al_Sharqi	Release	E20	2
E24	25.66276	36.76431	Al_Osh_Al_Sharqi	Release	E24	2
E13	25.66635	36.75909	Al_Osh_Al_Sharqi	Release	E13	2
E25	25.66656	36.76115	Al_Osh_Al_Sharqi	Release	E25	5
E26	25.57048	36.84659	QUMAN	Release	E26	5
E23	25.56002	36.83280	QUMAN	Release	E23	8
E12	25.55856	36.83240	QUMAN	Release	E12	2
E27	25.57091	36.84533	QUMAN	Release	E27	2
E22	25.56545	36.83597	QUMAN	Release	E22	5
E3	25.57069	36.84571	QUMAN	Release	E3	1
E4	25.56433	36.83623	QUMAN	Release	E4	8
E5	25.55808	36.83235	QUMAN	Release	E5	1
E7	25.56182	36.83370	QUMAN	Release	E7	5
E8	25.56285	36.83473	QUMAN	Release	E8	2
E28	25.49941	36.99894	Turtle_Bay	Release	E28	1

Array efficiency

Note:

More information on the differences between “Known missed events” and “Potentially missed events” can be found in the package vignettes.

The data used in this table is stored in the efficiency object.

These efficiency values are estimated using a simple step-by-step method (described in the package vignettes). In some situations, more advanced efficiency estimation methods may be required.

You can try running advEfficiency(results$efficiency) to obtain beta-drawn efficiency distributions (replace results with the name of the object where you saved the analysis).

Events recorded and missed

	Abu_Khalid	Abu_Laheq	Al_Osh_Al_Gharbi	Al_Osh_Al_Sharqi	QUMAN	Turtle_Bay
Recorded events	0	0	0	0	25	0
Known missed events	-	0	0	0	0	0
Potentially missed events	-	0	0	0	0	0

Array efficiency

Note: These values already include any intra-array efficiency estimates that have been requested.

	Abu_Khalid	Abu_Laheq	Al_Osh_Al_Gharbi	Al_Osh_Al_Sharqi	QUMAN	Turtle_Bay
Maximum efficiency	-	NaN%	NaN%	NaN%	100%	NaN%
Minimum efficiency	-	NaN%	NaN%	NaN%	100%	NaN%

Warning messages

Warning: Long array names detected. To improve graphic rendering, consider keeping array names under six characters.
Warning: Long section names detected. To improve graphic rendering, consider keeping section names under six characters.
Warning: The following station is listed in the deployments but is not part of the study's stations: 'AL1'
Discarding deployments at unknown stations.
Warning: 25 duplicated detections were found. Could an input file be duplicated?
Warning: No detections were found for receiver(s) 488907, 490788, 490791, 490792, 490793, 490794, 490795, 490796, 490797, 490798, 490799, 490800, 490801.
Warning: 'speed.warning'/'speed.error' were not set, skipping speed checks.
Warning: 'inactive.warning'/'inactive.error' were not set, skipping inactivity checks.

User comments

No comments were included during the analysis.

Biometric graphics

Note:

The data used in this graphic is the data present in the biometrics.csv file.

Last seen

Note:

The data used in this table and graphic is stored in the last.seen object.

	Disap. in Abu_Khalid	Disap. in Abu_Laheq	Disap. in Al_Osh_Al_Gharbi	Disap. in Al_Osh_Al_Sharqi	Disap. in QUMAN	Disap. in Turtle_Bay	Disap. at Release
Wild	0	0	0	0	25	0	28

Average time of arrival at each Array

Note:

Coloured lines on the outer circle indicate the mean value for each group and the respective ranges show the standard error of the mean. Each group’s bars sum to 100%. The number of data points in each group is presented between brackets in the legend of each pannel.

You can replicate these graphics and edit them as needed using the plotTimes() function.

The data used in these graphics is stored in the array.times object.

To obtain reports with the legacy linear circular scale, run options(actel.circular.scale = "linear") before running your analyses.

/var/folders/g0/3c99gfyx58141kbqt5_m0dk80000gn/T//Rtmp7IjzOY/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png

Time details for each section

Arrival days at each section

Note:

The data used in these graphics is stored in the section.times$arrival object.

Arrival times at each section

Note:

Coloured lines on the outer circle indicate the mean value for each group and the respective ranges show the standard error of the mean. Each group’s bars sum to 100%. The number of data points in each group is presented between brackets in the legend of each pannel.

You can replicate these graphics and edit them as needed using the plotTimes() function.

The data used in these graphics is stored in the section.times$arrival object.

To obtain reports with the legacy linear circular scale, run options(actel.circular.scale = "linear") before running your analyses.

/var/folders/g0/3c99gfyx58141kbqt5_m0dk80000gn/T//Rtmp7IjzOY/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png

Departure days at each section

Note:

The data used in these graphics is stored in the section.times$departure object.

Departure times at each section

Note:

Coloured lines on the outer circle indicate the mean value for each group and the respective ranges show the standard error of the mean. Each group’s bars sum to 100%. The number of data points in each group is presented between brackets in the legend of each pannel.

You can replicate these graphics and edit them as needed using the plotTimes() function.

The data used in these graphics is stored in the section.times$departure object.

To obtain reports with the legacy linear circular scale, run options(actel.circular.scale = "linear") before running your analyses.

/var/folders/g0/3c99gfyx58141kbqt5_m0dk80000gn/T//Rtmp7IjzOY/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png

Global residency

Note:

The data used in these graphics is stored in the global.ratios and time.positions objects.

You can replicate these graphics and edit them as needed using the plotRatios() function.

This data is also available split by group in the group.ratiosobject.

You can plot these results by group using the ‘group’ argument in plotRatios().

Absolutes

Percentages

Individual residency plots

Note:

The data used in these graphics is stored in the time.ratios object (one table per tag). More condensed information can be found in the section.movements object.

You can replicate these graphics and edit them as needed using the plotResidency() function.

Individual detection plots

Note:

You can choose to plot detections by station or by array using the detections.y.axis argument.

The detections are coloured by section. The vertical black dashed line shows the release time. The full dark-grey line shows the movement events considered valid, while the dashed dark-grey line shows the movement events considered invalid.

Manually edited tags are highlighted with yellow graphic borders.

Manually overridden tags are highlighted with red graphic borders.

The arrays have been aligned by section, following the order provided either in the spatial input or the section.order argument.

You can replicate these graphics and edit them as needed using the plotDetections() function.

You can also see the movement events of multiple tags simultaneously using the plotMoves() function.

The data used in these graphics is stored in the detections and movements objects (and respective valid counterparts).

Full log

Actel R package report.
Version: 1.3.0

Target folder: /Users/brittneyscannell/Desktop/actel
Timestamp: 2025-01-06 13:37:51.357207
Function: residency()

M: 'report' option has been activated.
M: Importing data. This process may take a while.
M: Number of target tags: 53.
Warning: Long array names detected. To improve graphic rendering, consider keeping array names under six characters.
Warning: Long section names detected. To improve graphic rendering, consider keeping section names under six characters.
Warning: The following station is listed in the deployments but is not part of the study's stations: 'AL1'
Discarding deployments at unknown stations.
Warning: 25 duplicated detections were found. Could an input file be duplicated?
M: Removing duplicated detections from the analysis per user command.
M: Matching detections with deployment periods.
M: Number of ALS: 27 (of which 13 had no detections)
Warning: No detections were found for receiver(s) 488907, 490788, 490791, 490792, 490793, 490794, 490795, 490796, 490797, 490798, 490799, 490800, 490801.
M: Data time range: 2022-11-28 14:20:06 to 2024-10-02 14:33:45 (Asia/Riyadh).
M: Data successfully imported!
M: Creating movement records for the valid tags.
M: Checking movement events quality.
Warning: 'speed.warning'/'speed.error' were not set, skipping speed checks.
Warning: 'inactive.warning'/'inactive.error' were not set, skipping inactivity checks.
M: Compiling and checking section movements for the valid tags.
M: Filtering valid array movements.
M: Filtering valid section movements.
M: Compiling residency objects.
M: Calculating daily locations for each tag.
M: Calculating inter-array efficiency.
M: Saving results as 'actel_residency_results.RData'.
M: Producing the report.
M: Drawing individual detection graphics.
M: Drawing individual residency graphics.
M: Analysis completed!

-------------------
User interventions:
-------------------
b # dup. detections
y # save results?
-------------------
Residency function call:
-------------------
residency(tz = 'Asia/Riyadh', section.order = NULL, datapack = NULL, max.interval = 60, min.total.detections = 2, min.per.event = c(1, 1), start.time = NULL, stop.time = NULL, speed.method = c('last to first'), speed.warning = NULL, speed.error = NULL, jump.warning = 2, jump.error = 3, inactive.warning = NULL, exclude.tags = NULL, override = NULL, report = TRUE, auto.open = TRUE, discard.orphans = FALSE, discard.first = NULL, save.detections = FALSE, section.warning = 1, section.error = 1, timestep = 'days', replicates = NULL, inactive.error = NULL, GUI = 'never', save.tables.locally = FALSE, print.releases = TRUE, detections.y.axis = 'auto')
-------------------

Index:

Summary Study area Stations Deployments Release sites Array efficiency Warnings Comments Biometrics Last seen Array times Section times Global residency Individual residency Individual detections Full log